[BioC] Background correction with just a few spots

[January Weiner]

Dear all,

I have a set of "strange" microarrays (nylon membrane / radioactive
labels). The raw data contains signals for the gene probes (a small
microbial genome) and for a number of probes which constitute the
background. There is no background signal directly in the data (like
in regular microarray chips), and I would like to subtract background
that is calculated from these few "background spots". Currently, I
just subtract the average of the background spots from all the other
spots.

In limma, what would be the most appropriate way to do it?

Cheers,
j.

-- 
-------- Dr. January Weiner 3 --------------------------------------
Max Planck Institute for Infection Biology
Charitéplatz 1
D-10117 Berlin, Germany
Web   : www.mpiib-berlin.mpg.de
Tel     : +49-30-28460514